{"id":13650766,"url":"https://github.com/SpikeInterface/spikeinterface","last_synced_at":"2025-04-22T18:32:56.337Z","repository":{"id":37270232,"uuid":"196581117","full_name":"SpikeInterface/spikeinterface","owner":"SpikeInterface","description":"A Python-based module for creating flexible and robust spike sorting 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Domain-Specific Applications","Programming"],"sub_categories":["🧬 Biology \u0026 Medicine","Python"],"readme":"# SpikeInterface: a unified framework for spike sorting\n\n\u003ctable\u003e\n\u003ctr\u003e\n  \u003ctd\u003eLatest Release\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://pypi.org/project/spikeinterface/\"\u003e\n    \u003cimg src=\"https://img.shields.io/pypi/v/spikeinterface.svg\" alt=\"latest release\" /\u003e\n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eDocumentation\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://spikeinterface.readthedocs.io/\"\u003e\n    \u003cimg src=\"https://readthedocs.org/projects/spikeinterface/badge/?version=latest\" alt=\"latest documentation\" /\u003e\n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eLicense\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://github.com/SpikeInterface/spikeinterface/blob/master/LICENSE\"\u003e\n    \u003cimg src=\"https://img.shields.io/pypi/l/spikeinterface.svg\" alt=\"license\" /\u003e\n    \u003c/a\u003e\n\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n  \u003ctd\u003eBuild Status\u003c/td\u003e\n  \u003ctd\u003e\n    \u003ca href=\"https://github.com/SpikeInterface/spikeinterface/actions/workflows/full-test-with-codecov.yml/badge.svg\"\u003e\n    \u003cimg src=\"https://github.com/SpikeInterface/spikeinterface/actions/workflows/full-test-with-codecov.yml/badge.svg\" alt=\"CI build status\" /\u003e\n    \u003c/a\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\t\u003ctd\u003eCodecov\u003c/td\u003e\n\t\u003ctd\u003e\n\t\t\u003ca href=\"https://codecov.io/github/spikeinterface/spikeinterface\"\u003e\n\t\t\u003cimg src=\"https://codecov.io/gh/spikeinterface/spikeinterface/branch/main/graphs/badge.svg\" alt=\"codecov\" /\u003e\n\t\t\u003c/a\u003e\n\t\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/table\u003e\n\n[![Twitter](https://img.shields.io/badge/@spikeinterface-%231DA1F2.svg?style=for-the-badge\u0026logo=Twitter\u0026logoColor=white)](https://twitter.com/spikeinterface) [![Mastodon](https://img.shields.io/badge/-@spikeinterface-%232B90D9?style=for-the-badge\u0026logo=mastodon\u0026logoColor=white)](https://fosstodon.org/@spikeinterface)\n\n\n\u003e :rocket::rocket::rocket:\n\u003e **New features!**: after months of development and testing, we are happy to announce that\n\u003e the latest release (0.101.0) includes a major API improvement: the `SortingAnalyzer`!\n\u003e To read more about why we did this, checkout the\n\u003e [SpikeInterface Enhancement Proposal](https://github.com/SpikeInterface/spikeinterface/issues/2282).\n\u003e Please follow this guide to transition from the old API to the new one:\n\u003e [Updating from legacy](https://spikeinterface.readthedocs.io/en/0.101.0/tutorials/waveform_extractor_to_sorting_analyzer.html).\n\n\nSpikeInterface is a Python framework designed to unify preexisting spike sorting technologies into a single code base.\n\nPlease [Star](https://github.com/SpikeInterface/spikeinterface/stargazers) the project to support us and [Watch](https://github.com/SpikeInterface/spikeinterface/subscription) to always stay up-to-date!\n\n\nWith SpikeInterface, users can:\n\n- read/write many extracellular file formats.\n- pre-process extracellular recordings.\n- run many popular, semi-automatic spike sorters (also in Docker/Singularity containers).\n- post-process sorted datasets.\n- compare and benchmark spike sorting outputs.\n- compute quality metrics to validate and curate spike sorting outputs.\n- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)\n- export a report and/or export to phy\n- offer a powerful Qt-based viewer in a separate package [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui)\n- have powerful sorting components to build your own sorter.\n\n\n## Documentation\n\nDetailed documentation of the latest PyPI release of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/stable).\n\nDetailed documentation of the development version of SpikeInterface can be found [here](https://spikeinterface.readthedocs.io/en/latest).\n\nSeveral tutorials to get started can be found in [spiketutorials](https://github.com/SpikeInterface/spiketutorials).\n\nCheckout our YouTube channel for video tutorials: [SpikeInterface YouTube Channel](https://www.youtube.com/@Spikeinterface).\n\nThere are also some useful notebooks [on our blog](https://spikeinterface.github.io) that cover advanced benchmarking\nand sorting components.\n\nYou can also have a look at the [spikeinterface-gui](https://github.com/SpikeInterface/spikeinterface-gui).\n\n\n## How to install spikeinterface\n\nYou can install the latest version of `spikeinterface` version with pip (using quotes ensures `pip install` works in all terminals/shells):\n\n```bash\npip install \"spikeinterface[full]\"\n```\n\nThe `[full]` option installs all the extra dependencies for all the different sub-modules.\n\nTo install all interactive widget backends, you can use:\n\n```bash\n pip install \"spikeinterface[full,widgets]\"\n```\n\n\nTo get the latest updates, you can install `spikeinterface` from source:\n\n```bash\ngit clone https://github.com/SpikeInterface/spikeinterface.git\ncd spikeinterface\npip install -e .\ncd ..\n```\n\n\n## Citation\n\nIf you find SpikeInterface useful in your research, please cite:\n\n```bibtex\n@article{buccino2020spikeinterface,\n  title={SpikeInterface, a unified framework for spike sorting},\n  author={Buccino, Alessio Paolo and Hurwitz, Cole Lincoln and Garcia, Samuel and Magland, Jeremy and Siegle, Joshua H and Hurwitz, Roger and Hennig, Matthias H},\n  journal={Elife},\n  volume={9},\n  pages={e61834},\n  year={2020},\n  publisher={eLife Sciences Publications Limited}\n}\n```\n\nPlease also cite other relevant papers for the specific components you use.\nFor a ful list of references, please check the [references](https://spikeinterface.readthedocs.io/en/latest/references.html) page.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSpikeInterface%2Fspikeinterface","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FSpikeInterface%2Fspikeinterface","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSpikeInterface%2Fspikeinterface/lists"}